rs9966950

Variant names:

• chr18-11304692-A-C
• rs9966950

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0461 in 152,268 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.046 (220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7022 AN: 152148 Hom.: 220 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.00876

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0449

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0461 AC: 7024 AN: 152268 Hom.: 220 Cov.: 32 AF XY: 0.0446 AC XY: 3322 AN XY: 74452

African (AFR) AF: 0.0625 AC: 2597 AN: 41526

American (AMR) AF: 0.0373 AC: 571 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0524 AC: 253 AN: 4826

European-Finnish (FIN) AF: 0.00876 AC: 93 AN: 10622

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0456 AC: 3100 AN: 68026

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0432 Hom.: 15

Bravo AF: 0.0482

Asia WGS AF: 0.0240 AC: 84 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9966950; hg19: chr18-11304691;